The cake layers play a key role in the rejection of particles in dynamic membrane bioreactors and produces most of the resistance. This research aims to directly observe and measure the transient structure of the cake layers at different times and depths. The results showed the membrane flux remained relatively stable for the first 30 h, but decreased from 110 L/m² h to 88 L/m² h in the next 20 h. The membrane resistance was highly correlated with the cake layer thickness. The porosity and average pore diameter obtained from the scanning electron microcopy (SEM) pictures displayed no temporal variations, as only the new generated surface of the cake layer can be observed by SEM. However, the specific pore volume and surface area based on the Brunauer–Emmett–Teller (BET) nitrogen adsorption results displayed an initial decline, from 0.30 cc/g to 0.22 cc/g, due to the disappearance of the small diameter pores (1–10 nm) with time. The large diameter pores (30–250 nm) accounted for the majority of the cumulative pore volumes in all samples, as well as in the top layer, middle layer, and bottom layer. The specific pore volume and specific surface area exhibited a decline from the top layer to bottom layer, from 0.38 cc/g to 0.21 cc/g, due to the blockage of large diameter pores. In addition, BET nitrogen adsorption data provided comprehensive structural characteristics of the cake layers.